MLPA (multiplex ligation-dependent probe amplification) and MS-MLPA (methylation- specific MLPA) have rapidly evolved as promising methods for copy number variation and DNA methylation studies. The goal of this proposal is to continue the development of software for genomic and methylation-specific MLPA probe design. We have developed H-MAPD, a web based probe design tool that automates the generation and selection of probes for human genomic MLPA. We propose to expand the software in two ways: 1) To extend H-MAPD to support mouse and rat genomic MLPA probe design. 2) To develop a separate tool to handle MS-MLPA probe design. One major obstacle for MLPA and MS-MLPA is the difficulty in probe design. By automating the tedious probe design process, our software will become a valuable tool in the implementation of MLPA and MS-MLPA. PUBLIC HEALTH RELEVANCE: An increasing number of human diseases are now known to be associated with copy number variation and/or aberrant DNA methylation. The proposed software provides a computational tool that will facilitate research in these two areas.